Pathology Atlas - Appendix E

Automatically prompt the user to activate the current project, if it does not appear to already be activated? This is mainly useful to help ensure that calls to renv::snapshot() and renv::restore() use the project library. See ?renv::activate for more details.

NaN min

activate.prompt

logical[1]

true

Automatically snapshot changes to the project library after a new package is installed?

The default Bitbucket host to be used during package retrieval.

NaN min

bitbucket.host

character[1]

api.bitbucket.org/2.0

The method to use when attempting to copy directories. See Copy Methods for more information.

The amount of time to spend (in seconds) when attempting to download a file. Only applicable when the curl downloader is used.

The number of times to attempt re-downloading a file, when transient download errors occur. Only applicable when the curl downloader is used.

Enable the global renv package cache? When active, renv will install packages into a global cache, and link or copy packages from the cache into your library as appropriate. This can greatly save on disk space and install time when packages are shared across multiple projects in the same environment.

Symlink packages from the global renv package cache into your project library? When TRUE, renv will use symlinks (or, on Windows, junction points) to reference packages installed in the cache. Set this to FALSE if you’d prefer to copy packages from the cache into your project library.

Many renv APIs require the enumeration of your project’s package dependencies. This option controls how errors that occur during this enumeration are handled. By default, errors are reported but are non-fatal. Set this to "fatal" to force errors to be fatal, and "ignored" to ignore errors altogether. See [dependencies()] for more details.

When library(renv) is called, should its exports be placed on the search path? Set this to FALSE to avoid issues that can arise with, for example, renv::load() masking base::load(). In general, we recommend referencing renv functions from its namespace explicitly; e.g. prefer renv::snapshot() over snapshot(). By default, all exported renv functions are attached and placed on the search path, for backwards compatibility with existing scripts using renv.

A character vector of external libraries, to be used in tandem with your projects. Be careful when using external libraries: it’s possible that things can break within a project if the version(s) of packages used in your project library happen to be incompatible with packages in your external libraries; for example, if your project required xyz 1.0 but xyz 1.1 was present and loaded from an external library. Can also be an function that provides the paths to external libraries. Library paths will be expanded via [.expand_R_libs_env_var()] as necessary.

Enable the renv file-backed cache? When enabled, renv will cache the contents of files that are read (e.g. DESCRIPTION files) in memory, thereby avoiding re-reading the file contents from the filesystem if the file has not changed. renv uses the file mtime to determine if the file has changed; consider disabling this if mtime is unreliable on your system.

The default GitHub host to be used during package retrieval.

The default GitLab host to be used during package retrieval.

A character vector of library paths, to be used by [hydrate()] when attempting to hydrate projects. When empty, the default set of library paths (as documented in ?hydrate) are used instead. See [hydrate()] for more details.

Allow for a set of ‘shortcuts’ when installing packages with renv? When enabled, if renv discovers that a package to be installed is already available within the user or site libraries, then it will install a local copy of that package.

DEPRECATED: Please use renv.config.install.transactional instead.

Perform a transactional install of packages during install and restore? When enabled, renv will first install packages into a temporary library, and later copy or move those packages back into the project library only if all packages were successfully downloaded and installed. This can be useful if you’d like to avoid mutating your project library if installation of one or more packages fails.

NaN min

install.transactional

logical[1]

true

Be verbose when installing R packages from sources? When TRUE, renv will stream any output generated during package build + installation to the console.

Use interprocess locks when invoking methods which might mutate the project library? Enable this to allow multiple processes to use the same renv project, while minimizing risks relating to concurrent access to the project library. Disable this if you encounter locking issues. Locks are stored as files within the project at renv/lock; if you need to manually remove a stale lock you can do so via unlink("renv/lock", recursive = TRUE).

Attempt to download binaries from MRAN during restore? See vignette("mran", package = "renv") for more details.

Override the R package repositories used during [restore()]? Primarily useful for deployment / continuous integration, where you might want to enforce the usage of some set of repositories over what is defined in renv.lock or otherwise set by the R session.

Boolean; enable RSPM integration for renv projects? When TRUE, renv will attempt to transform the repository URLs used by RSPM into binary URLs as appropriate for the current platform. Set this to FALSE if you’d like to continue using source-only RSPM URLs, or if you find that renv is improperly transforming your repository URLs.

Enable sandboxing for renv projects? When active, renv will attempt to sandbox the system library, preventing non-system packages installed in the system library from becoming available in renv projects. (That is, only packages with priority "base" or "recommended", as reported by installed.packages(), are made available.) Sandboxing is done by linking or copying system packages into a separate library path, and then instructing R to use that library path as the system library path. In some environments, this action can take a large amount of time – in such a case, you may want to disable the renv sandbox.

Should renv shims be installed on package load? When enabled, renv will install its own shims over the functions install.packages(), update.packages() and remove.packages(), delegating these functions to [renv::install()], [renv::update()] and [renv::remove()] as appropriate.

Validate package dependencies when calling snapshot? When TRUE, renv will attempt to diagnose potential issues in the project library before creating renv.lock – for example, if a package installed in the project library depends on a package which is not currently installed.

Be quiet during startup? When set, renv will not display the typical Project <path> loaded. [renv <version>] banner on startup.

Check that the project library is synchronized with the lockfile on load?

Check for package updates when the session is initialized? This can be useful if you’d like to ensure that your project lockfile remains up-to-date with packages as they are released on CRAN.

Check for package updates in parallel? This can be useful when a large number of packages installed from non-CRAN remotes are installed, as these packages can then be checked for updates in parallel.

Include the user library on the library paths for your projects? Note that this risks breaking project encapsulation and is not recommended for projects which you intend to share or collaborate on with other users. See also the caveats for the renv.config.external.libraries option.

Load the user R profile (typically located at ~/.Rprofile) when renv is loaded? Consider disabling this if you require extra encapsulation in your projects; e.g. if your .Rprofile attempts to load packages that you might not install in your projects.